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Lau AY. Enhanced sampling of glutamate receptor ligand-binding domains. Neurosci Lett 2019; 700:17-21. [DOI: 10.1016/j.neulet.2018.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023]
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2
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Yu A, Salazar H, Plested AJR, Lau AY. Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics. Neuron 2017; 97:139-149.e4. [PMID: 29249286 PMCID: PMC5766834 DOI: 10.1016/j.neuron.2017.11.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/26/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) mediate neurotransmission at the majority of excitatory synapses in the brain. Little is known, however, about how glutamate reaches the recessed binding pocket in iGluR ligand-binding domains (LBDs). Here we report the process of glutamate binding to a prototypical iGluR, GluA2, in atomistic detail using unbiased molecular simulations. Charged residues on the LBD surface form pathways that facilitate glutamate binding by effectively reducing a three-dimensional diffusion process to a spatially constrained, two-dimensional one. Free energy calculations identify residues that metastably bind glutamate and help guide it into the binding pocket. These simulations also reveal that glutamate can bind in an inverted conformation and also reorient while in its pocket. Electrophysiological recordings demonstrate that eliminating these transient binding sites slows activation and deactivation, consistent with slower glutamate binding and unbinding. These results suggest that binding pathways have evolved to optimize rapid responses of AMPA-type iGluRs at synapses.
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Affiliation(s)
- Alvin Yu
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Héctor Salazar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Andrew J R Plested
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany.
| | - Albert Y Lau
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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3
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Karlov DS, Lavrov MI, Palyulin VA, Zefirov NS. MM-GBSA and MM-PBSA performance in activity evaluation of AMPA receptor positive allosteric modulators. J Biomol Struct Dyn 2017; 36:2508-2516. [DOI: 10.1080/07391102.2017.1360208] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Dmitry S. Karlov
- Department of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991 Russian Federation
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region 142432, Russian Federation
| | - Mstislav I. Lavrov
- Department of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991 Russian Federation
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region 142432, Russian Federation
| | - Vladimir A. Palyulin
- Department of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991 Russian Federation
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region 142432, Russian Federation
| | - Nikolay S. Zefirov
- Department of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991 Russian Federation
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region 142432, Russian Federation
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Pairas GN, Perperopoulou F, Tsoungas PG, Varvounis G. The Isoxazole Ring and ItsN-Oxide: A Privileged Core Structure in Neuropsychiatric Therapeutics. ChemMedChem 2017; 12:408-419. [DOI: 10.1002/cmdc.201700023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/13/2017] [Indexed: 01/23/2023]
Affiliation(s)
- George N. Pairas
- Laboratory of Medicinal Chemistry, Department of Pharmacy; University of Patras; 265 04 Patras Greece
| | - Fereniki Perperopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology; Agricultural University of Athens; 75 Iera Odos St. 118 55 Athens Greece
| | - Petros G. Tsoungas
- Laboratory of Biochemistry; Hellenic Pasteur Institute; 127 Vas. Sofias Ave. 115 21 Athens Greece
| | - George Varvounis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry; University of Ioannina; 451 10 Ioannina Greece
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Martins ACV, de-Lima-Neto P, Caetano EWS, Freire VN. An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework. NEW J CHEM 2017. [DOI: 10.1039/c6nj03939a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.
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Affiliation(s)
- A. C. V. Martins
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - P. de-Lima-Neto
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - E. W. S. Caetano
- Federal Institute of Education
- Science and Technology of Ceara
- 60040-531 Fortaleza
- Brazil
| | - V. N. Freire
- Department of Physics
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
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Guo Y, Wolter T, Kubař T, Sumser M, Trauner D, Elstner M. Molecular Dynamics Investigation of gluazo, a Photo-Switchable Ligand for the Glutamate Receptor GluK2. PLoS One 2015; 10:e0135399. [PMID: 26308344 PMCID: PMC4550381 DOI: 10.1371/journal.pone.0135399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 07/21/2015] [Indexed: 11/25/2022] Open
Abstract
Photochromic ligands (PCLs), defined as photoswitchable molecules that are able to endow native receptors with a sensitivity towards light, have become a promising photopharmacological tool for various applications in biology. In general, PCLs consist of a ligand of the target receptor covalently linked to an azobenzene, which can be reversibly switched between two configurations upon light illumination. Gluazo, as a PCL that targets excitatory amino acid receptors, in its dark-adapted trans iso-form was characterized to be a partial agonist of the kainate glutamate receptor GluK2. Application of UV light leads to the formation of the cis form, with remarkedly reduced affinity towards GluK2. The mechanism of the change of ligand affinity induced by the photoisomerization was unresolved. The presented computational study explains how the isomerization of such a PCL affects the structural changes in the target receptor that lead to its activation.
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Affiliation(s)
- Yanan Guo
- Department of Theoretical Chemical Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Tino Wolter
- Department of Theoretical Chemical Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Tomáš Kubař
- Department of Theoretical Chemical Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Martin Sumser
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Butenandtstr. 5–13, 81377 Munich, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Butenandtstr. 5–13, 81377 Munich, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
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Song B, Sun Q, Li H, Ge B, Pan JS, Wee ATS, Zhang Y, Huang S, Zhou R, Gao X, Huang F, Fang H. Irreversible Denaturation of Proteins through Aluminum‐Induced Formation of Backbone Ring Structures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bo Song
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Qian Sun
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Haikuo Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Ji Sheng Pan
- Institute of Materials Research and Engineering, Singapore 117602 (Republic of Singapore)
| | - Andrew Thye Shen Wee
- Physics Department, National University of Singapore, Singapore 117542 (Republic of Singapore)
| | - Yong Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China)
| | - Shaohua Huang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 (China)
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, New York, NY 10598 (USA)
| | - Xingyu Gao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Fang Huang
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Haiping Fang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
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Song B, Sun Q, Li H, Ge B, Pan JS, Wee ATS, Zhang Y, Huang S, Zhou R, Gao X, Huang F, Fang H. Irreversible Denaturation of Proteins through Aluminum‐Induced Formation of Backbone Ring Structures. Angew Chem Int Ed Engl 2014; 53:6358-63. [PMID: 24777568 DOI: 10.1002/anie.201307955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/24/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Bo Song
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Qian Sun
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Haikuo Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Ji Sheng Pan
- Institute of Materials Research and Engineering, Singapore 117602 (Republic of Singapore)
| | - Andrew Thye Shen Wee
- Physics Department, National University of Singapore, Singapore 117542 (Republic of Singapore)
| | - Yong Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China)
| | - Shaohua Huang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 (China)
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, New York, NY 10598 (USA)
| | - Xingyu Gao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
| | - Fang Huang
- Center for Bioengineering and Biotechnology, China University of Petroleum (Huadong), Changjiang West Road 66, Qingdao 266580 (China)
| | - Haiping Fang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800‐204, Shanghai 201800 (China)
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Wolter T, Steinbrecher T, Trauner D, Elstner M. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain. PLoS One 2014; 9:e92716. [PMID: 24713651 PMCID: PMC3979659 DOI: 10.1371/journal.pone.0092716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/24/2014] [Indexed: 11/18/2022] Open
Abstract
Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs). We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.
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Affiliation(s)
- Tino Wolter
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Thomas Steinbrecher
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Munich, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
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Heinzelmann G, Chen PC, Kuyucak S. Computation of standard binding free energies of polar and charged ligands to the glutamate receptor GluA2. J Phys Chem B 2014; 118:1813-24. [PMID: 24479628 DOI: 10.1021/jp412195m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurate calculation of the binding affinity of small molecules to proteins has the potential to become an important tool in rational drug design. In this study, we use the free energy perturbation (FEP) method with restraints to calculate the standard binding free energy of five ligands (ACPA, AMPA, CNQX, DNQX, and glutamate) to the glutamate receptor GluA2, which plays an essential role in synaptic transmission. To deal with the convergence problem in FEP calculations with charged ligands, we use a protocol where the ligand is coupled in the binding site while it is decoupled in bulk solution simultaneously. The contributions from the conformational, rotational, and translational entropies to the standard binding free energy are determined by applying/releasing respective restraints to the ligand in bulk/binding site. We also employ the confine-and-release approach, which helps to resolve convergence problems in FEP calculations. Our results are in good agreement with the experimental values for all five ligands, including the charged ones which are often problematic in FEP calculations. We also analyze the different contributions to the binding free energy of each ligand to GluA2 and discuss the nature of these interactions.
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Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics. Structure 2013; 21:1788-99. [PMID: 23972471 PMCID: PMC3814224 DOI: 10.1016/j.str.2013.07.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/11/2013] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
Abstract
The NMDA receptor family of glutamate receptor ion channels is formed by obligate heteromeric assemblies of GluN1, GluN2, and GluN3 subunits. GluN1 and GluN3 bind glycine, whereas GluN2 binds glutamate. Crystal structures of the GluN1 and GluN3A ligand-binding domains (LBDs) in their apo states unexpectedly reveal open- and closed-cleft conformations, respectively, with water molecules filling the binding pockets. Computed conformational free energy landscapes for GluN1, GluN2A, and GluN3A LBDs reveal that the apo-state LBDs sample closed-cleft conformations, suggesting that their agonists bind via a conformational selection mechanism. By contrast, free energy landscapes for the AMPA receptor GluA2 LBD suggest binding of glutamate via an induced-fit mechanism. Principal component analysis reveals a rich spectrum of hinge bending, rocking, twisting, and sweeping motions that are different for the GluN1, GluN2A, GluN3A, and GluA2 LBDs. This variation highlights the structural complexity of signaling by glutamate receptor ion channels.
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